chr19-44953923-T-C

Variant names:

• chr19-44953923-T-C
• rs3760627
• ENST00000591646.1:n.85A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000591646.1(ENSG00000267114):​n.85A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,846 control chromosomes in the GnomAD database, including 20,147 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.51 (20147 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENSG00000267114 ENST00000591646.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737
• Publications: 32 publications found

Genes affected

ENSG00000267114 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000591646.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267114	ENST00000591646.1	TSL:3	n.85A>G		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77290 AN: 151726 Hom.: 20114 Cov.: 31

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.490

GnomAD2 exomes AF: 0.800 AC: 8 AN: 10 AF XY: 0.750

Gnomad FIN exome AF: 0.500

Gnomad NFE exome AF: 0.875

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.510 AC: 77371 AN: 151844 Hom.: 20147 Cov.: 31 AF XY: 0.512 AC XY: 37991 AN XY: 74188

African (AFR) AF: 0.579 AC: 23958 AN: 41372

American (AMR) AF: 0.566 AC: 8617 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1544 AN: 3464

East Asian (EAS) AF: 0.552 AC: 2856 AN: 5174

South Asian (SAS) AF: 0.580 AC: 2793 AN: 4814

European-Finnish (FIN) AF: 0.489 AC: 5159 AN: 10554

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30905 AN: 67922

Other (OTH) AF: 0.491 AC: 1037 AN: 2112

Alfa AF: 0.477 Hom.: 58312

Bravo AF: 0.518

Asia WGS AF: 0.577 AC: 2007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.43
PhyloP100		-0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3760627; hg19: chr19-45457180;